1
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Sandoval-Velasco M, Dudchenko O, Rodríguez JA, Pérez Estrada C, Dehasque M, Fontsere C, Mak SST, Khan R, Contessoto VG, Oliveira Junior AB, Kalluchi A, Zubillaga Herrera BJ, Jeong J, Roy RP, Christopher I, Weisz D, Omer AD, Batra SS, Shamim MS, Durand NC, O'Connell B, Roca AL, Plikus MV, Kusliy MA, Romanenko SA, Lemskaya NA, Serdyukova NA, Modina SA, Perelman PL, Kizilova EA, Baiborodin SI, Rubtsov NB, Machol G, Rath K, Mahajan R, Kaur P, Gnirke A, Garcia-Treviño I, Coke R, Flanagan JP, Pletch K, Ruiz-Herrera A, Plotnikov V, Pavlov IS, Pavlova NI, Protopopov AV, Di Pierro M, Graphodatsky AS, Lander ES, Rowley MJ, Wolynes PG, Onuchic JN, Dalén L, Marti-Renom MA, Gilbert MTP, Aiden EL. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell 2024; 187:3541-3562.e51. [PMID: 38996487 DOI: 10.1016/j.cell.2024.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 03/07/2024] [Accepted: 06/03/2024] [Indexed: 07/14/2024]
Abstract
Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.
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Affiliation(s)
| | - Olga Dudchenko
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
| | - Juan Antonio Rodríguez
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain
| | - Cynthia Pérez Estrada
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Marianne Dehasque
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - Ruqayya Khan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Achyuth Kalluchi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Bernardo J Zubillaga Herrera
- Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA
| | - Jiyun Jeong
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Renata P Roy
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Departments of Biology and Physics, Texas Southern University, Houston, TX 77004, USA
| | - Ishawnia Christopher
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sanjit S Batra
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neva C Durand
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alfred L Roca
- Department of Animal Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mariya A Kusliy
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | | | - Natalya A Lemskaya
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | | | - Svetlana A Modina
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | - Elena A Kizilova
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | | | - Nikolai B Rubtsov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Gur Machol
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Krisha Rath
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009, Australia
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Rob Coke
- San Antonio Zoo, San Antonio, TX 78212, USA
| | | | | | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia and Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | | | | | - Naryya I Pavlova
- Institute of Biological Problems of Cryolitezone SB RAS, Yakutsk 677000, Russia
| | - Albert V Protopopov
- Academy of Sciences of Sakha Republic, Yakutsk 677000, Russia; North-Eastern Federal University, Yakutsk 677027, Russia
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA
| | | | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA
| | - Love Dalén
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marc A Marti-Renom
- Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain; Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain; ICREA, 08010 Barcelona, Spain; Universitat Pompeu Fabra, 08002 Barcelona, Spain.
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway.
| | - Erez Lieberman Aiden
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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2
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Dehasque M, Morales HE, Díez-Del-Molino D, Pečnerová P, Chacón-Duque JC, Kanellidou F, Muller H, Plotnikov V, Protopopov A, Tikhonov A, Nikolskiy P, Danilov GK, Giannì M, van der Sluis L, Higham T, Heintzman PD, Oskolkov N, Gilbert MTP, Götherström A, van der Valk T, Vartanyan S, Dalén L. Temporal dynamics of woolly mammoth genome erosion prior to extinction. Cell 2024; 187:3531-3540.e13. [PMID: 38942016 DOI: 10.1016/j.cell.2024.05.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/08/2024] [Accepted: 05/17/2024] [Indexed: 06/30/2024]
Abstract
A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.
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Affiliation(s)
- Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
| | - Hernán E Morales
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Patrícia Pečnerová
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 11418 Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Héloïse Muller
- Master de Biologie, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon I, Universite de Lyon, 69007 Lyon, France
| | - Valerii Plotnikov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Yakutsk, Republic of Sakha (Yakutia), Russia
| | - Albert Protopopov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Yakutsk, Republic of Sakha (Yakutia), Russia
| | - Alexei Tikhonov
- Zoological Institute of Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Pavel Nikolskiy
- Geological Institute of the Russian Academy of Sciences, Moscow, Russia
| | - Gleb K Danilov
- Peter the Great Museum of Anthropology and Ethnography, Kunstkamera, Russian Academy of Sciences, 3 University Embankment, Box 199034, Saint-Petersburg, Russia
| | - Maddalena Giannì
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Laura van der Sluis
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Tom Higham
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Peter D Heintzman
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 11418 Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; SciLifeLab, Stockholm, Sweden
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
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3
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Baker KH, Gray HWI, Lister AM, Spassov N, Welch AJ, Trantalidou K, De Cupere B, Bonillas E, De Jong M, Çakırlar C, Sykes N, Hoelzel AR. Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial. Sci Rep 2024; 14:3015. [PMID: 38346983 PMCID: PMC10861457 DOI: 10.1038/s41598-023-48112-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/22/2023] [Indexed: 02/15/2024] Open
Abstract
Anthropogenic factors have impacted the diversity and evolutionary trajectory of various species. This can be through factors such as pressure on population size or range, habitat fragmentation, or extensive manipulation and translocation. Here we use time-calibrated data to better understand the pattern and processes of evolution in the heavily manipulated European fallow deer (Dama dama). During the Pleistocene, fallow deer had a broad distribution across Europe and were found as far north as Britain during the Eemian interglacial. The last glacial period saw fallow deer retreat to southern refugia and they did not disperse north afterwards. Their recolonisation was mediated by people and, from northern Europe and the British Isles, fallow deer were transported around the world. We use ancient and modern mitochondrial DNA (mtDNA) and mitogenomic data from Eemian Britain to assess the pattern of change in distribution and lineage structure across Europe over time. We find founder effects and mixed lineages in the northern populations, and stability over time for populations in southern Europe. The Eemian sample was most similar to a lineage currently in Italy, suggesting an early establishment of the relevant refuge. We consider the implications for the integration of anthropogenic and natural processes towards a better understanding of the evolution of fallow deer in Europe.
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Affiliation(s)
- K H Baker
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - H W I Gray
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - A M Lister
- Natural History Museum, London, SW7 5BD, UK
| | - N Spassov
- National Museum of Natural History at the Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - A J Welch
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - K Trantalidou
- Hellenic Ministry of Culture, 5 Themistokleous Str., 10677, Athens, Greece
| | - B De Cupere
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - E Bonillas
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - M De Jong
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - C Çakırlar
- Groningen Institute of Archaeology, University of Groningen, Poststraat 6, 9712 NL, Groningen, The Netherlands
| | - N Sykes
- Department of Archaeology and History, University of Exeter, Exeter, UK
| | - A R Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK.
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4
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Pečnerová P, Lord E, Garcia-Erill G, Hanghøj K, Rasmussen MS, Meisner J, Liu X, van der Valk T, Santander CG, Quinn L, Lin L, Liu S, Carøe C, Dalerum F, Götherström A, Måsviken J, Vartanyan S, Raundrup K, Al-Chaer A, Rasmussen L, Hvilsom C, Heide-Jørgensen MP, Sinding MHS, Aastrup P, Van Coeverden de Groot PJ, Schmidt NM, Albrechtsen A, Dalén L, Heller R, Moltke I, Siegismund HR. Population genomics of the muskox' resilience in the near absence of genetic variation. Mol Ecol 2024; 33:e17205. [PMID: 37971141 DOI: 10.1111/mec.17205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/07/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.
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Affiliation(s)
- Patrícia Pečnerová
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Zoo, Frederiksberg, Denmark
| | - Edana Lord
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Genís Garcia-Erill
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Malthe Sebro Rasmussen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaodong Liu
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Cindy G Santander
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Long Lin
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fredrik Dalerum
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Biodiversity Research Institute (CSIC-UO-PA), Mieres, Spain
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johannes Måsviken
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo, Russian Academy of Sciences, Magadan, Russia
| | | | - Amal Al-Chaer
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Linett Rasmussen
- Copenhagen Zoo, Frederiksberg, Denmark
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Mads Peter Heide-Jørgensen
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Greenland Institute of Natural Resources, Copenhagen, Denmark
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Peter Aastrup
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | | | - Niels Martin Schmidt
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hans Redlef Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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5
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Díez-Del-Molino D, Dehasque M, Chacón-Duque JC, Pečnerová P, Tikhonov A, Protopopov A, Plotnikov V, Kanellidou F, Nikolskiy P, Mortensen P, Danilov GK, Vartanyan S, Gilbert MTP, Lister AM, Heintzman PD, van der Valk T, Dalén L. Genomics of adaptive evolution in the woolly mammoth. Curr Biol 2023; 33:1753-1764.e4. [PMID: 37030294 DOI: 10.1016/j.cub.2023.03.084] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/24/2023] [Accepted: 03/29/2023] [Indexed: 04/10/2023]
Abstract
Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.
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Affiliation(s)
- David Díez-Del-Molino
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
| | - Marianne Dehasque
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patrícia Pečnerová
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alexei Tikhonov
- Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | | | | | - Foteini Kanellidou
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, 119017 Moscow, Russia
| | - Peter Mortensen
- Department of Zoology, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - Gleb K Danilov
- Peter the Great Museum of Anthropology and Ethnography, Kunstkamera, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A. Shilo, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), 685000 Magadan, Russia
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway
| | | | - Peter D Heintzman
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, 11418 Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Science for Life Laboratory, 17165 Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
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6
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Lord E, Marangoni A, Baca M, Popović D, Goropashnaya AV, Stewart JR, Knul MV, Noiret P, Germonpré M, Jimenez EL, Abramson NI, Vartanyan S, Prost S, Smirnov NG, Kuzmina EA, Olsen RA, Fedorov VB, Dalén L. Population dynamics and demographic history of Eurasian collared lemmings. BMC Ecol Evol 2022; 22:126. [PMID: 36329382 PMCID: PMC9632076 DOI: 10.1186/s12862-022-02081-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species. RESULTS Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene. CONCLUSIONS This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.
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Affiliation(s)
- Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 10691, Stockholm, Sweden. .,Department of Zoology, Stockholm University, 10691, Stockholm, Sweden. .,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden.
| | - Aurelio Marangoni
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 10691, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden
| | - Mateusz Baca
- Centre of New Technologies, University of Warsaw, S. Banacha 2C, 02-097, Warsaw, Poland
| | - Danijela Popović
- Centre of New Technologies, University of Warsaw, S. Banacha 2C, 02-097, Warsaw, Poland
| | - Anna V Goropashnaya
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775-7000, USA
| | - John R Stewart
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, BH12 5BB, Dorset, UK
| | - Monika V Knul
- Department of Archaeology, Anthropology and Geography, University of Winchester, Winchester, SO22 4NR, UK
| | - Pierre Noiret
- Service de Préhistoire, Université de Liège, Place du 20 Août 7, 4000, Liège, Belgium
| | - Mietje Germonpré
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, Brussels, Belgium
| | - Elodie-Laure Jimenez
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, Brussels, Belgium.,School of Geosciences, University of Aberdeen, Aberdeen, Scotland
| | - Natalia I Abramson
- Department of Molecular Systematics, Zoological Institute RAS, St Petersburg, Russia
| | - Sergey Vartanyan
- Far East Branch, N.A. Shilo North-East Interdisciplinary Scientific Research Institute Russian Academy of Sciences (NEISRI FEB RAS), 685000, Magadan, Russia
| | - Stefan Prost
- Central Research Laboratories, Natural History Museum Vienna, 1010, Vienna, Austria.,Department of Cognitive Biology, University of Vienna, 1090, Vienna, Austria.,Konrad Lorenz Institute of Ethology, 1160, Vienna, Austria.,South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Nickolay G Smirnov
- Institute of Plant and Animal Ecology UB RAS, Russian Academy of Sciences, 202 8 Marta Street, 620144, Ekaterinburg, Russia
| | - Elena A Kuzmina
- Institute of Plant and Animal Ecology UB RAS, Russian Academy of Sciences, 202 8 Marta Street, 620144, Ekaterinburg, Russia
| | - Remi-André Olsen
- Science for Life Laboratory (SciLifeLab), Dept of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Vadim B Fedorov
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775-7000, USA
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 10691, Stockholm, Sweden. .,Department of Zoology, Stockholm University, 10691, Stockholm, Sweden. .,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden.
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7
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Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA. Genes (Basel) 2022; 13:genes13040687. [PMID: 35456493 PMCID: PMC9032354 DOI: 10.3390/genes13040687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.
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8
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Blattner L, Lucek K, Beck N, Berner D, Fumetti S. Intra‐Alpine Islands: Population genomic inference reveals high degree of isolation between freshwater spring habitats. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Lucas Blattner
- Department of Environmental Sciences, Geoecology University of Basel Basel Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, Plant Ecology and Evolution University of Basel Basel Switzerland
| | - Nathanael Beck
- Department of Environmental Sciences, Geoecology University of Basel Basel Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Animal Diversity and Evolution University of Basel Basel Switzerland
| | - Stefanie Fumetti
- Department of Environmental Sciences, Geoecology University of Basel Basel Switzerland
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9
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Murchie TJ, Monteath AJ, Mahony ME, Long GS, Cocker S, Sadoway T, Karpinski E, Zazula G, MacPhee RDE, Froese D, Poinar HN. Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA. Nat Commun 2021; 12:7120. [PMID: 34880234 PMCID: PMC8654998 DOI: 10.1038/s41467-021-27439-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada.
| | - Alistair J Monteath
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.,School of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
| | - Matthew E Mahony
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - George S Long
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Scott Cocker
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Tara Sadoway
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,The Hospital for Sick Children, Toronto, Canada
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Whitehorse, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, United States
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada. .,Department of Biochemistry, McMaster University, Hamilton, Canada. .,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada. .,CIFAR Humans and the Microbiome Program, Toronto, Canada.
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10
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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11
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Rey-Iglesia A, Lister AM, Campos PF, Brace S, Mattiangeli V, Daly KG, Teasdale MD, Bradley DG, Barnes I, Hansen AJ. Exploring the phylogeography and population dynamics of the giant deer ( Megaloceros giganteus) using Late Quaternary mitogenomes. Proc Biol Sci 2021; 288:20201864. [PMID: 33977786 PMCID: PMC8114472 DOI: 10.1098/rspb.2020.1864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 04/15/2021] [Indexed: 12/20/2022] Open
Abstract
Late Quaternary climatic fluctuations in the Northern Hemisphere had drastic effects on large mammal species, leading to the extinction of a substantial number of them. The giant deer (Megaloceros giganteus) was one of the species that became extinct in the Holocene, around 7660 calendar years before present. In the Late Pleistocene, the species ranged from western Europe to central Asia. However, during the Holocene, its range contracted to eastern Europe and western Siberia, where the last populations of the species occurred. Here, we generated 35 Late Pleistocene and Holocene giant deer mitogenomes to explore the genetics of the demise of this iconic species. Bayesian phylogenetic analyses of the mitogenomes suggested five main clades for the species: three pre-Last Glacial Maximum clades that did not appear in the post-Last Glacial Maximum genetic pool, and two clades that showed continuity into the Holocene. Our study also identified a decrease in genetic diversity starting in Marine Isotope Stage 3 and accelerating during the Last Glacial Maximum. This reduction in genetic diversity during the Last Glacial Maximum, coupled with a major contraction of fossil occurrences, suggests that climate was a major driver in the dynamics of the giant deer.
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Affiliation(s)
- Alba Rey-Iglesia
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark
| | - Adrian M. Lister
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Paula F. Campos
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, 4450-208 Matosinhos, Portugal
| | - Selina Brace
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Kevin G. Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Matthew D. Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Ian Barnes
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Anders J. Hansen
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark
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12
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Million-year-old DNA sheds light on the genomic history of mammoths. Nature 2021; 591:265-269. [PMID: 33597750 PMCID: PMC7116897 DOI: 10.1038/s41586-021-03224-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/11/2021] [Indexed: 11/17/2022]
Abstract
Temporal genomic data hold great potential for studying evolutionary processes, including speciation. However, sampling across speciation events would in many cases require genomic time series that stretch well into the Early Pleistocene (>1 million years). Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far is from a 560-780 ka old horse specimen2. Here we report the recovery of genome-wide data from three Early and Middle Pleistocene mammoth specimens, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these gave rise to the woolly mammoth, whereas the other represents a previously unrecognised lineage that was ancestral to the first mammoths to colonise North America. Our analyses reveal that the North American Columbian mammoth traces its ancestry to a Middle Pleistocene hybridisation between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were present already a million years ago. These findings highlight the potential of deep time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
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13
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Fry E, Kim SK, Chigurapti S, Mika KM, Ratan A, Dammermann A, Mitchell BJ, Miller W, Lynch VJ. Functional Architecture of Deleterious Genetic Variants in the Genome of a Wrangel Island Mammoth. Genome Biol Evol 2021; 12:48-58. [PMID: 32031213 PMCID: PMC7094797 DOI: 10.1093/gbe/evz279] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2019] [Indexed: 12/21/2022] Open
Abstract
Woolly mammoths were among the most abundant cold-adapted species during the Pleistocene. Their once-large populations went extinct in two waves, an end-Pleistocene extinction of continental populations followed by the mid-Holocene extinction of relict populations on St. Paul Island ∼5,600 years ago and Wrangel Island ∼4,000 years ago. Wrangel Island mammoths experienced an episode of rapid demographic decline coincident with their isolation, leading to a small population, reduced genetic diversity, and the fixation of putatively deleterious alleles, but the functional consequences of these processes are unclear. Here, we show that a Wrangel Island mammoth genome had many putative deleterious mutations that are predicted to cause diverse behavioral and developmental defects. Resurrection and functional characterization of several genes from the Wrangel Island mammoth carrying putatively deleterious substitutions identified both loss and gain of function mutations in genes associated with developmental defects (HYLS1), oligozoospermia and reduced male fertility (NKD1), diabetes (NEUROG3), and the ability to detect floral scents (OR5A1). These data suggest that at least one Wrangel Island mammoth may have suffered adverse consequences from reduced population size and isolation.
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Affiliation(s)
- Erin Fry
- Department of Human Genetics, The University of Chicago
| | - Sun K Kim
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University
| | | | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia
| | | | - Brian J Mitchell
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University
| | - Webb Miller
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University
| | - Vincent J Lynch
- Department of Biological Sciences, University at Buffalo, SUNY
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14
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Gaitán-Espitia JD, Hobday AJ. Evolutionary principles and genetic considerations for guiding conservation interventions under climate change. GLOBAL CHANGE BIOLOGY 2021; 27:475-488. [PMID: 32979891 DOI: 10.1111/gcb.15359] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/26/2020] [Indexed: 05/25/2023]
Abstract
Impacts of climate change are apparent in natural systems around the world. Many species are and will continue to struggle to persist in their current location as their preferred environment changes. Traditional conservation efforts aiming to prevent local extinctions have focused on two aspects that theoretically enhance genetic diversity-population connectivity and population size-through 'passive interventions' (such as protected areas and connectivity corridors). However, the exceptionally rapid loss of biodiversity that we are experiencing as result of anthropogenic climate change has shifted conservation approaches to more 'active interventions' (such as rewilding, assisted gene flow, assisted evolution, artificial selection, genetic engineering). We integrate genetic/genomic approaches into an evolutionary biology framework in order to discuss with scientists, conservation managers and decision makers about the opportunities and risks of interventions that need careful consideration in order to avoid unwanted evolutionary outcomes.
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Affiliation(s)
- Juan D Gaitán-Espitia
- CSIRO Oceans and Atmosphere, Hobart, Tas., Australia
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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15
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Dussex N, Alberti F, Heino MT, Olsen RA, van der Valk T, Ryman N, Laikre L, Ahlgren H, Askeyev IV, Askeyev OV, Shaymuratova DN, Askeyev AO, Döppes D, Friedrich R, Lindauer S, Rosendahl W, Aspi J, Hofreiter M, Lidén K, Dalén L, Díez-Del-Molino D. Moose genomes reveal past glacial demography and the origin of modern lineages. BMC Genomics 2020; 21:854. [PMID: 33267779 PMCID: PMC7709250 DOI: 10.1186/s12864-020-07208-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/29/2020] [Indexed: 12/31/2022] Open
Abstract
Background Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America. Results We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines. Conclusions Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07208-3.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden. .,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-10405, Stockholm, Sweden. .,Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden.
| | - Federica Alberti
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Reiss-Engelhorn-Museen, Zeughaus C5, 68159, Mannheim, Germany
| | - Matti T Heino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-10405, Stockholm, Sweden.,Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland.,History, Culture and Communication Studies, University of Oulu, P.O. Box 1000, 90014, Oulu, Finland
| | - Remi-Andre Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-17121, Solna, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-10405, Stockholm, Sweden
| | - Nils Ryman
- Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden
| | - Linda Laikre
- Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden
| | - Hans Ahlgren
- Department of Archeology and Classical studies, Stockholm University, SE-10691, Stockholm, Sweden
| | - Igor V Askeyev
- The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, 420087, Kazan, Russia
| | - Oleg V Askeyev
- The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, 420087, Kazan, Russia
| | - Dilyara N Shaymuratova
- The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, 420087, Kazan, Russia
| | - Arthur O Askeyev
- The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, 420087, Kazan, Russia
| | - Doris Döppes
- Reiss-Engelhorn-Museen, Zeughaus C5, 68159, Mannheim, Germany
| | - Ronny Friedrich
- Curt-Engelhorn-Center Archaeometry, C4, 8, D-68159, Mannheim, Germany
| | - Susanne Lindauer
- Curt-Engelhorn-Center Archaeometry, C4, 8, D-68159, Mannheim, Germany
| | - Wilfried Rosendahl
- Reiss-Engelhorn-Museen, Zeughaus C5, 68159, Mannheim, Germany.,Curt-Engelhorn-Center Archaeometry, C4, 8, D-68159, Mannheim, Germany
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Kerstin Lidén
- Department of Archeology and Classical studies, Stockholm University, SE-10691, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-10405, Stockholm, Sweden
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden. .,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-10405, Stockholm, Sweden. .,Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden.
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16
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Larsson P, von Seth J, Hagen IJ, Götherström A, Androsov S, Germonpré M, Bergfeldt N, Fedorov S, Eide NE, Sokolova N, Berteaux D, Angerbjörn A, Flagstad Ø, Plotnikov V, Norén K, Díez-Del-Molino D, Dussex N, Stanton DWG, Dalén L. Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190212. [PMID: 31679495 PMCID: PMC6863501 DOI: 10.1098/rstb.2019.0212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'
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Affiliation(s)
- Petter Larsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Mietje Germonpré
- Operational Direction 'Earth and History of Life', Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Nora Bergfeldt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sergey Fedorov
- Mammoth Museum of Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk, Republic Sakha (Yakutia), Russia
| | - Nina E Eide
- Norwegian Institute for Nature Research, Trondheim, Norway
| | - Natalia Sokolova
- Arctic Research Station of Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences, Yamal-Nenets Autonomous District, Russia.,Arctic Research Center of Yamal-Nenets Autonomous District, Salekhard, Russia
| | - Dominique Berteaux
- Canada Research Chair on Northern Biodiversity and Centre for Northern Studies, Université du Québec à Rimouski, Rimouski, Canada
| | | | | | - Valeri Plotnikov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Republic of Sakha, Yakutia, Russia
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - David Díez-Del-Molino
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Nicolas Dussex
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
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17
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Ngatia JN, Lan TM, Dinh TD, Zhang L, Ahmed AK, Xu YC. Signals of positive selection in mitochondrial protein-coding genes of woolly mammoth: Adaptation to extreme environments? Ecol Evol 2019; 9:6821-6832. [PMID: 31380018 PMCID: PMC6662336 DOI: 10.1002/ece3.5250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 11/25/2022] Open
Abstract
The mammoths originated in warm and equatorial Africa and later colonized cold and high-latitude environments. Studies on nuclear genes suggest that woolly mammoth had evolved genetic variations involved in processes relevant to cold tolerance, including lipid metabolism and thermogenesis, and adaptation to extremely varied light and darkness cycles. The mitochondria is a major regulator of cellular energy metabolism, thus the mitogenome of mammoths may also exhibit adaptive evolution. However, little is yet known in this regard. In this study, we analyzed mitochondrial protein-coding genes (MPCGs) sequences of 75 broadly distributed woolly mammoths (Mammuthus primigenius) to test for signatures of positive selection. Results showed that a total of eleven amino acid sites in six genes, namely ND1, ND4, ND5, ND6, CYTB, and ATP6, displayed strong evidence of positive selection. Two sites were located in close proximity to proton-translocation channels in mitochondrial complex I. Biochemical and homology protein structure modeling analyses demonstrated that five amino acid substitutions in ND1, ND5, and ND6 might have influenced the performance of protein-protein interaction among subunits of complex I, and three substitutions in CYTB and ATP6 might have influenced the performance of metabolic regulatory chain. These findings suggest metabolic adaptations in the mitogenome of woolly mammoths in relation to extreme environments and provide a basis for further tests on the significance of the variations on other systems.
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Affiliation(s)
| | - Tian Ming Lan
- BGI‐ShenzhenShenzhenChina
- Laboratory of Genomics and Molecular Biomedicine, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- China National Genebank, BGI‐ShenzhenShenzhenChina
| | - Thi Dao Dinh
- College of Wildlife ResourcesNortheast Forestry UniversityHarbinChina
| | - Le Zhang
- College of Wildlife ResourcesNortheast Forestry UniversityHarbinChina
| | | | - Yan Chun Xu
- College of Wildlife ResourcesNortheast Forestry UniversityHarbinChina
- State Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and UtilizationHarbinChina
- State Forestry and Grassland Administration Detecting Centre of WildlifeHarbinChina
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18
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Hoelzel AR, Bruford MW, Fleischer RC. Conservation of adaptive potential and functional diversity. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01151-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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19
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Full Mitogenomes in the Critically Endangered Kākāpō Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity. Genes (Basel) 2018; 9:genes9040220. [PMID: 29671759 PMCID: PMC5924562 DOI: 10.3390/genes9040220] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 12/02/2022] Open
Abstract
Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal approaches can help us understand the effects of population declines on genetic diversity in real time. Sequencing pre-decline as well as post-decline mitogenomes representing all the remaining mitochondrial diversity, we estimated the loss of genetic diversity in the critically endangered kākāpō (Strigops habroptilus). We detected a signal of population expansion coinciding with the end of the Pleistocene last glacial maximum (LGM). Also, we found some evidence for northern and southern lineages, supporting the hypothesis that the species may have been restricted to isolated northern and southern refugia during the LGM. We observed an important loss of neutral genetic diversity associated with European settlement in New Zealand but we could not exclude a population decline associated with Polynesian settlement in New Zealand. However, we did not find evidence for fixation of deleterious mutations. We argue that despite high pre-decline genetic diversity, a rapid and range-wide decline combined with the lek mating system, and life-history traits of kākāpō contributed to a rapid loss of genetic diversity following severe population declines.
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